Constructing Metabolic Models
Running metabolic modeling workflows in KBase
KBase has a suite of Apps and data that support the reconstruction, prediction, and design of metabolic models in bacteria, fungi, and plants using functionality from ModelSEED and PlantSEED databases. Genome-scale metabolic models are primarily reconstructed from protein functional annotations. These genome-scale metabolic models can be used to explore an organism’s growth in specific media conditions, determine which biochemical pathways are present, optimize production of an important metabolite, identify high flux pathways, and more.
Metabolic models can be used to evaluate an organism’s metabolic capability by simulating growth under different conditions to answer important biological questions such as:
- What biochemical pathways are present?
- What are the high flux pathways under a certain growth condition?
- Could the organism grow anaerobically?
- Would it grow under certain minimal media conditions?
- Could the organism be optimized to produce a particular drug molecule or industrially important biofuel?
- Microbial Metabolic Model Reconstruction and Analysis Tutorial – Guides through a workflow on how to draft a metabolic model and use KBase Apps to gapfill, run flux balance analysis and simulate growth.
- Modeling and Integration of Omics Data in KBase – Demonstrates model construction, integration of transcriptomics and metabolomics data, and an example of data representation on metabolic maps based on a Yeast example.
- Predicting Novel Compounds and Reactions using PickAxe – Demonstrates cheminformatics expansion of known metabolites, based on compounds within a metabolic model, and using the PickAxe App to map metabolomics data.
Build Metabolic Model Tutorial
Introduction to Metabolic Modeling in KBase